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    METHODS FOR DETECTION OF DONOR-DERIVED CELL-FREE DNA IN TRANSPLANT RECIPIENTS OF MULTIPLE ORGANS
    12.
    发明公开
    METHODS FOR DETECTION OF DONOR-DERIVED CELL-FREE DNA IN TRANSPLANT RECIPIENTS OF MULTIPLE ORGANS 审中-公开

    公开(公告)号：US20240229136A9

    公开(公告)日：2024-07-11

    申请号：US18279006

    申请日：2022-02-24

    Applicant: Natera, Inc.

    Inventor： Zachary DEMKO ,  Ebad AHMED ,  Ryan SWENERTON ,  Paul VAN HUMMELEN

    IPC: C12Q1/6883 ,  C12Q1/6869

    CPC classification number: C12Q1/6883 ,  C12Q1/6869 ,  C12Q2600/156

    Abstract: The present disclosure provides methods of amplifying and sequencing DNA, comprising: extracting cell-free DNA from a blood, plasma, serum or urine sample of a transplant recipient who has received transplantation of one or more organs including simultaneous or sequential transplantation of multiple organs, wherein the extracted cell-free DNA comprises donor-derived cell-free DNA and recipient-derived cell-free DNA; performing targeted amplification at 200-50,000 target loci in a single reaction volume using 200-50,000 primer pairs, wherein the target loci comprise polymorphic loci and non-polymorphic loci; sequencing the amplification products by high-throughput sequencing to obtain a sequencing reads and quantifying the amount of donor-derived cell-free DNA and the amount of total cell-free DNA based on the sequencing reads; and determining whether the amount of donor-derived cell-free DNA or a function thereof exceeds a cutoff threshold indicating transplant rejection or graft injury.

    METHODS FOR CANCER DETECTION AND MONITORING
    14.
    发明申请
    METHODS FOR CANCER DETECTION AND MONITORING 有权

    公开(公告)号：US20220056509A1

    公开(公告)日：2022-02-24

    申请号：US17461298

    申请日：2021-08-30

    Applicant: Natera, Inc.

    Inventor： Bernhard ZIMMERMANN ,  Raheleh SALARI ,  Ryan SWENERTON ,  Hsin-Ta WU ,  Himanshu SETHI

    IPC: C12Q1/6827 ,  C12Q1/6886

    Abstract: The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided. For example, provided here is a method for monitoring and detection of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer, comprising generating a set of amplicons by performing a multiplex amplification reaction on nucleic acids isolated from a sample of blood or urine or a fraction thereof from a patient who has been treated for a breast cancer, bladder cancer, or colorectal cancer, wherein each amplicon of the set of amplicons spans at least one single nucleotide variant locus of a set of patient-specific single nucleotide variant loci associated with the breast cancer, bladder cancer, or colorectal cancer; and determining the sequence of at least a segment of each amplicon of the set of amplicons that comprises a patient-specific single nucleotide variant locus, wherein detection of one or more patient-specific single nucleotide variants is indicative of early relapse or metastasis of breast cancer, bladder cancer, or colorectal cancer.

    METHODS FOR DETECTING IMMUNE CELL DNA AND MONITORING IMMUNE SYSTEM
    15.
    发明申请
    METHODS FOR DETECTING IMMUNE CELL DNA AND MONITORING IMMUNE SYSTEM 有权

    公开(公告)号：US20220251654A1

    公开(公告)日：2022-08-11

    申请号：US17616536

    申请日：2020-05-29

    Applicant: Natera, Inc.

    Inventor： Dina M. HAFEZ ,  Prashanthi NATARAJAN ,  Raheleh SALARI ,  Ryan SWENERTON ,  Bernhard ZIMMERMANN

    IPC: C12Q1/6881

    Abstract: The disclosure herein provides methods and compositions for detecting or monitoring immune cell populations in biological samples. The methods and compositions disclosed herein are particularly useful for detecting or monitoring immune cell populations in patients suffering from a disease or undergoing treatment of a disease resulting in depletion of immune cells. In particular, the present disclosure provides method for using multiplex PCR combined with next-generation DNA sequencing to detect DNA containing recombined V(D)J gene segments which can be used to detect immune cells.

    METHODS AND SYSTEMS FOR CALLING MUTATIONS
    17.
    发明申请
    METHODS AND SYSTEMS FOR CALLING MUTATIONS 有权

    公开(公告)号：US20210257048A1

    公开(公告)日：2021-08-19

    申请号：US16972930

    申请日：2019-06-12

    Applicant: Natera, Inc.

    Inventor： Bernhard ZIMMERMANN ,  Raheleh SALARI ,  Ryan SWENERTON ,  Dina M. HAFEZ

    IPC: G16B20/20 ,  C12Q1/6886

    Abstract: A method for calling a mutation includes determining, for each target base of a plurality of target bases, a respective value for a background error parameter based on training data. The method further includes determining a motif-specific error model including the background error parameter by performing processes that include: identifying a respective motif for each target base of the plurality of target bases, grouping the plurality of target bases into a plurality of groups, each group corresponding to a particular motif, and determining, for each group, a respective motif-specific parameter value for the background error parameter based on the determined values for the background error parameter for the target bases included in each group. The method further includes calling a mutation using the motif-specific error model and sequencing information for a biological sample.

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